Scanning probe with twin-nanopore or a-single-nanopore for sensing biomolecules

ABSTRACT

A mechanism is provided for sensing molecules. A twin-nanopore probe includes a first channel and a second channel. A first pressure-controlled reservoir is connected to the first channel to generate a positive pressure. A second pressure-controlled reservoir is connected to the second channel to generate a negative pressure. A container includes ionic solvent with molecules, and a tip of the twin-nanopore probe is submerged in the container of the ionic fluid with the molecules. The first channel, the second channel, the first pressure-controlled reservoir, and the second pressure-controlled reservoir are filled with the ionic fluid. The first pressure-controlled reservoir drives the ionic fluid out of the first channel and the second pressure-controlled reservoir draws in the ionic fluid with the molecules and solvent through the second channel. A flow of ionic current in the twin-nanopore probe is measured to differentiate the molecules that flow through the second channel.

BACKGROUND

The present invention relates to sensing molecules, and morespecifically, to a scanning twin-nanopore probe for sensing molecules.

Nanopore sequencing is a method for determining the order in whichnucleotides occur on a strand of deoxyribonucleic acid (DNA). A nanopore(also referred to a pore, nanochannel, hole, etc.) can be a small holein the order of several nanometers in internal diameter. The theorybehind nanopore sequencing is about what occurs when the nanopore issubmerged in a conducting fluid and an electric potential (voltage) isapplied across the nanopore. Under these conditions, a slight electriccurrent due to conduction of ions through the nanopore can be measured,and the amount of current is very sensitive to the size and shape of thenanopore. If single bases or strands of DNA pass (or part of the DNAmolecule passes) through the nanopore, this can create a change in themagnitude of the current through the nanopore. Other electrical oroptical sensors can also be positioned around the nanopore so that DNAbases can be differentiated while the DNA passes through the nanopore.

The DNA can be driven through the nanopore by using various methods, sothat the DNA might eventually pass through the nanopore. The scale ofthe nanopore can have the effect that the DNA may be forced through thehole as a long string, one base at a time, like thread through the eyeof a needle. Recently, there has been growing interest in applyingnanopores as sensors for rapid analysis of biomolecules such asdeoxyribonucleic acid (DNA), ribonucleic acid (RNA), protein, etc.Special emphasis has been given to applications of nanopores for DNAsequencing, as this technology holds the promise to reduce the cost ofsequencing below $1000/human genome.

SUMMARY

According to an embodiment, a method for sensing molecules is provided.A twin-nanopore probe has a first channel and a second channel. Thefirst pressure-controlled reservoir is connected to the first channel,and the first pressure-controlled reservoir generates a positivepressure. A second pressure-controlled reservoir is connected to thesecond channel, and the second pressure-controlled reservoir generates anegative pressure. A container includes ionic fluid with molecules, anda tip of the twin-nanopore probe is submerged in the container of theionic solvent with the molecules. The first channel, the second channel,the first pressure-controlled reservoir, and the secondpressure-controlled reservoir are filled with the ionic fluid. The firstpressure-controlled reservoir drives ionic fluid out of the firstchannel, and the second pressure-controlled reservoir draws in the ionicfluid with the molecules and solvent through the second channel. A flowof ionic current in the twin-nanopore probe is measured to differentiatethe molecules that flow through the second channel.

According to an embodiment, a method for sensing molecules is provided.A single-nanopore probe includes a channel, and a reservoir is connectedto the channel. A container includes ionic fluid with molecules, and atip of the single-nanopore probe is submerged in the container of theionic fluid with the molecules. The channel and the reservoir are filledwith the ionic fluid. A negative pressure inside the single-nanoporeprobe draws the molecules into channel. A flow of ionic current throughthe single-nanopore probe is measured to differentiate the moleculesthat flow into the channel.

According to an embodiment, a system for sensing molecules is provided.A twin-nanopore probe includes a first channel and a second channel. Afirst pressure-controlled reservoir is connected to the first channel,and the first pressure-controlled reservoir is configured to generate apositive pressure. A second pressure-controlled reservoir is connectedto the second channel, and the second pressure-controlled reservoir isconfigured to generate a negative pressure. A container includes ionicsolvent with molecules, and a tip of the twin-nanopore probe issubmerged in the container of the ionic fluid with the molecules. Thefirst channel, the second channel, the first pressure-controlledreservoir, and the second pressure-controlled reservoir are filled withthe ionic fluid. The first pressure-controlled reservoir is configuredto drive the ionic fluid out of the first channel, and the secondpressure-controlled reservoir is configured to draw in the ionic fluidwith the molecules and solvent through the second channel. Thetwin-nanopore probe is configured to facilitate a flow of ionic currentthat is measured to differentiate the molecules that flow through thesecond channel.

According to an embodiment, a system for sensing molecules is provided.A single-nanopore probe includes a channel, and a reservoir is connectedto the channel. A container includes ionic fluid with molecules, and atip of the single-nanopore probe is submerged in the container of theionic fluid with the molecules. The channel and the reservoir are filledwith the ionic fluid. A negative pressure inside the single-nanoporeprobe is configured to draw the molecules into channel. Thesingle-nanopore probe is configured to facilitate a flow of ioniccurrent that is measured to differentiate the molecules that flow intothe second channel.

Additional features and advantages are realized through the techniquesof the present invention. Other embodiments and aspects of the inventionare described in detail herein and are considered a part of the claimedinvention. For a better understanding of the invention with theadvantages and the features, refer to the description and to thedrawings.

BRIEF DESCRIPTION OF THE SEVERAL VIEWS OF THE DRAWINGS

The subject matter which is regarded as the invention is particularlypointed out and distinctly claimed in the claims at the conclusion ofthe specification. The forgoing and other features, and advantages ofthe invention are apparent from the following detailed description takenin conjunction with the accompanying drawings in which:

FIG. 1 is a cross-sectional view of a system having a twin-nanoporeprobe structure for sensing biomolecules according to an embodiment.

FIGS. 2A through 2F illustrate views of fabricating the twin-nanoporeprobe according to an embodiment, in which:

FIG. 2A illustrates a cross-sectional view of a structure in the processof being fabricated into the twin-nanopore probe;

FIG. 2B illustrates a top view of the structure with two nanotubesadded;

FIG. 2C illustrates a cross-sectional view of the structure with anelectrically insulating material of layer deposited;

FIG. 2D illustrates a top view of the structure after selective etching;

FIG. 2E illustrates a top view of the structure resulting in thetwin-nanopore probe; and

FIG. 2F illustrates a cross-sectional view of the twin-nanopore probeflipped and mounted on a holder.

FIG. 3 is a cross-sectional view of a system having a single-nanoporeprobe structure for sensing biomolecules according to an embodiment.

FIG. 4 is a cross-sectional view of the system having the twin-nanoporeprobe structure in which the nanopores are coated with an organic layeraccording to an embodiment.

FIG. 5 is a cross-sectional view of a system having the single-nanoporeprobe structure in which the nanopore is coated with an organic layeraccording to an embodiment.

FIG. 6 is a flow diagram illustrating a method of sensing molecules viaa twin-nanopore probe structure according to an embodiment.

FIG. 7 is a flow diagram illustrating a method of sensing molecules viaa single-nanopore probe structure according to an embodiment.

FIG. 8 is a block diagram that illustrates an example of a computer(computer setup) having capabilities, which may be included in and/orcombined with embodiments.

DETAILED DESCRIPTION

The present disclosure provides a mechanism to sense biomolecules usinga twin-nanopore probe and ionic current measurements.

Highly negatively charged DNA molecules can be electrically driventhrough a pore of a few nanometers in diameter (nanopore). Nanoporeshave been proposed or demonstrated as sensors for rapid analysis ofbiomolecules (DNA, RNA, proteins, etc.) or their interactions. Theseconventional approaches require a relative large volume of samples(order of 10 μL (microliters)) and apply only on sensing chargedmolecules as the molecules are driven through the nanopore viaelectrical field.

An embodiment provides a twin-nanopore probe structure in which anactive flow of ionic buffer is driven from one nanopore to anothernanopore by pressure instead of electrical field. This allows thetwin-nanopore probe to apply to both charged and non-charged moleculesand the twin-nanopore probe can measure the local (10 nm (nanometers) tomicrons away from the probe (i.e., localized area)). As this probe isactively scanning every area in the ionic buffer with molecules to bemeasured, the concentration of molecules is completely unlimited.

Now turning to the figures, FIG. 1 is a cross-sectional view of a system100 having a schematic of the twin-nanopore probe structure for sensingbiomolecules according to an embodiment.

The twin-nanopore probe 101 is a scanning probe made of electricallyinsulating material. The twin-nanopore probe 101 is made of two hollowchannels 102 and 103. Both hollow channels 102 and 103 gradually taperinto two nanopores 104 and 105 (respectively) at the sharp end of thetwin-nanopore probe 101. The twin-nanopore probe 101 scans (e.g., backand forth, left to right, and/or up and down) in a container 106. Thecontainer 106 is filled with ionic solvent 107 (which may be ionicfluid) and with molecules 108 and 109 that need to be sensed.

Two pressure-controlled reservoirs 110 and 111 are filled with ionicbuffer 120 and then connected (forming a seal) to the hollow channels102 and 103 respectively. Each pressure-controlled reservoir 110 and 111may be a syringe pump, mechanical pump, motorized pump, etc. Thescanning twin-nanopore probe 101 is dipped into the solvent 107(containing molecules 108 and 109) in the container 106 to sense themolecules 108 and 109 near the twin-nanopore probe 101, e.g., near thenanopore 104 and/or nanopore 105. The pressure-controlled reservoir 110pressure-drives the ionic buffer 120 inside reservoir 110 into thehollow channel 102, and the ionic buffer 120 flows from the reservoir110 into the container 106 and locally mixes with the solvent 107.Concurrently, the mixed ionic buffer 120 (together with molecules 108and 109) in the container 106 is pressure driven into hollow channel 103through the nanopore 105 and flows into the pressure-controlledreservoir 111 by applying a negative pressure in reservoir 111. The flowdirections (caused by the positive pressure of the reservoir 110 and thenegative pressure of the reservoir 111) of the ionic buffer 120 areindicated by arrows 112 and 113. Depending on the ratio of the flow rateof pressures 112 and 113, a flow profile will form in a region of thecontainer 106, defined as area 118 (i.e., region within the container106). Molecules 108 and 109 inside the area 118 are pulled (one at atime) into the nanopore 105 for sensing by the combination of thepositive pressure 112 and the negative pressure 113.

In one case, the ionic buffer 120 in the pressure-controlled reservoirs110 and 111 may be different than the solvent 107 in the container 106.For example, when the solvent 107 is a non-conductive solvent and whenthe ionic buffer 120 in pressure-controlled reservoirs 110 and 111 isconductive, the whole system can still work for detecting molecules 108and 109 using ionic current through nanopore 105. In another case, theionic buffer 120 in the pressure-controlled reservoirs 110 and 111 maybe the same as the solvent 107 (but the solvent 107 includes themolecules 108/109) in the container 106. For example, both the solvent107 and the ionic buffer 120 are conductive.

Electrochemical electrodes 114 and 115, such as Ag/AgCl wires, aredipped into the reservoirs 110 and 111 respectively. Voltage of voltagesource 116 is applied between the two electrodes 114 and 115 and theresulting ionic current is measured by ammeter 117.

While molecules 108 and 109 pass through nanopore 105, a change in theionic current (measured via ammeter 117 which may be connectedto/implemented in a computer 800 in FIG. 8) is detected. The amount ofchange in the measured ionic current depends on the size and surfacecharge of the molecule 108/109. In this way, each molecule 108/109 issensed as it passes through nanopore 105.

When no molecule 108 or 109 is in the nanopore 105 and voltage of thevoltage source 116 is applied, a baseline ionic current (baselinewaveform) flows from the electrode 114, through the reservoir 110 (i.e.,via ionic buffer 120), through the hollow channel 102 (i.e., via ionicbuffer 120), through nanopore 104 (i.e., via ionic buffer 120), out intothe mixed ionic buffer 120 (which has mixed with the solvent 107) in thecontainer 106 (only within a small distance around the tip of thetwin-nanopore probe 101), back into the nanopore 105, through the hollowchannel 103, into the reservoir 111, and into the electrode 115. Thebaseline ionic current is the measurement (via ammeter 117) when nomolecule 108 and 109 is in the nanopore 105.

However, when a molecule 108 or 109 is in the nanopore 105 and thevoltage of the voltage source 116 is applied, the ionic current(modulated waveform) flows from the electrode 114, through the reservoir110 (i.e., via ionic buffer 120), through the hollow channel 102,through nanopore 104, out into the mixed ionic buffer 120 in thecontainer 106 (only within a small distance around the tip of thetwin-nanopore probe 101), back into the nanopore 105 (in which the ioniccurrent is affected/changed by the particular molecule 108 or 109),through the hollow channel 103, into the reservoir 111, and into theelectrode 115 (to be measured by the ammeter 117).

As understood by one skilled in the art, the ionic buffer 120 conductselectricity (e.g., via ions) to produce the ionic current that ismeasured by the ammeter 117. FIG. 8 illustrates an example of a computer800 which may implement, control, and/or regulate the voltage of thevoltage source 116, measurements of the ammeter 117, and respectivepressures 112 and 113 of the pressure-controlled reservoirs 110 and 111.Also, the baseline waveform of the baseline ionic current and themodulated/changed waveform of the ionic current (affected by themolecule 108 or 109 inside the nanopore 105) can be displayed andrecorded by the computer 800. For example, a molecule 108 or 109 withinthe nanopore 105 may change/affect the magnitude and/or time duration ofthe measured ionic current, and this waveform (e.g., current on they-axis and time on the x-axis) is displayed on the display of thecomputer 800 for each measurement of the ionic current.

Note that ionic buffer 120 and solvent 107 could be the same or totallydifferent. In the case that 107 is non-conductive solvent, conductiveionic buffer 120 will still facilitate the flow of the ionic current(measured by ammeter 117) so that molecules 108 or 109 can still besensed.

Regarding the details of ionic current (measured by ammeter 117), whenvoltage of voltage source 116 is applied between two electrodes 114 and115(for example, positive terminal of the voltage is on electrode 114while the negative terminal of the voltage is on electrode 115) positiveions are driven from electrode 114 to the channel 102, then driven outof nanopore 104 into the area 118, then driven into nanopore 105 andinto channel 103, and then driven to reservoir 111 and onto electrode115 where the positive ions react with electrodes 115. Negative ions dothe reverse. This illustrates an example of how the measured ioniccurrent (measured by ammeter 117) forms.

In the system 100, each part of the ionic buffer/solution 120 inreservoir 110, channel 102, nanopore 104, area 118 (mixed in thecontainer 106), nanopore 105, channel 103, and reservoir 111 acts likeelectrical resistance in series. The resistances of the ionic buffer 120inside the nanopore 104 and 105 are orders of magnitude larger than theother parts (reservoir 110, channel 102, area 118, channel 103, andreservoir 111) as the nanopores 104 and 105 have the smallestcross-section (orders of magnitude smaller). As such, the ionic currentis mainly dependent on the sum of the resistance of the ionic buffer 120in nanopores 104 and 105. Consequently, only molecules 108 or 109 insidethe nanopore 104 or 105 can induce a large change of the baseline ioniccurrent (measured by ammeter 117). If one makes the size of the nanopore105 small enough so that only one molecule 108 or 109 can get in (i.e.,fit) at any given time (as discussed herein), the ionic current(measured by ammeter 117) has single molecule resolution.

FIGS. 2A through 2F (generally referred to as FIG. 2) illustrate viewsof fabricating the twin-nanopore probe 101 (and also a single-nanoporeprobe 301 shown in FIG. 3) according to an embodiment.

FIG. 2A is a cross-sectional view of a structure 200 that is in theprocess of being fabricated into the twin-nanopore probe 101. As shownin FIG. 2A, layer 201 is the substrate, such as a Si wafer. Layer 202 isa sacrificial material that can be easily etched later on, such as SiO₂.Layer 203 is an electrically insulating material, such as Si₃N₄. Theinsulating material of layer 203 is the housing for the twin-nanoporeprobe 101.

FIG. 2B is the top view of the structure 200. Two nanotubes 204 and 205are inserted/placed in the insulating material of layer 203. The twonanotubes 204 and 205 may be carbon nanotubes, glass nanotubes, etc. Thetwo nanotubes 204 and 205 overlaps each other (for example, 205 coverson top of 204). Later in the fabrication process, an etching step can bedone to cut the two nanotubes 204 and 205 at a location illustrated as206 (shown with dashed lines). Depending on where the location 206 ischosen, the distance between the ends of the two nanotubes 204 and 205at the cutting ends will vary. Note that when forming thesingle-nanopore probe 301, only one nanotube 204 (or 205) is inserted;otherwise, the fabrication process remains the same except one nanotube204 is being utilized.

FIG. 2C is a cross-sectional view of the structure 200. Before etching,an electrically insulating material of layer 207, such as Si₃N₄, isdeposited on top of the nanotubes 204 and 205 to seal the nanotubes 204and 205, as shown in FIG. 2C. Material of layer 207, nanotubes 204 and205 (at the location 206), and material of layer 203 are selectivelyetched via photolithography and reactive ion etching to provide theresult shown in FIG. 2D. FIG. 2D shows the resulting structure 200 inthe top view after utilizing a mask (not shown) to etch away material.In the structure 200, most of the area is etched down to the layer 202in the desired shape according to the mask, while rectangular areas 208and 209 are only etched down to layer 203 (via another mask not shown).

Then, all the material of layer 202 is etched away using a wet etchant,such as HF (hydrogen fluoride), and the completed twin-nanopore probe101 can be lifted off from the substrate layer 201, as shown in the topview of the structure 200 in FIG. 2E. The remaining parts of nanotubes204 and 205 are corresponding to nanopores 104 and 105 respectivelyshown in FIG. 1.

As shown in FIG. 2F (cross-sectional view), the twin-nanopore probe 101is flipped and mounted on a holder 210, which can be made of anyelectrically-insulating materials. An o-ring, glue, or epoxy can also beemployed to enhance the sealing between the twin-nanopore probe 101 andthe holder 210. Holes 211 and 212 can be made through the holder 210.One end of the hole 211 (or 212) is aligned to window area 208 (or 209),while the other end of the hole 211 (or 212) is adapted to a fluidictube 213 (or 214) to connect to the reservoirs 110 (or 111). The windowarea 208 (or 209), the hole 211 (or 212), and the fluidic tube 213 (or214) respectively correspond to the channel 102 (or 103) in FIG. 1.

FIG. 3 is a cross-sectional view of a system 300 having a schematic of asingle-nanopore probe 301 structure for sensing biomolecules accordingto an embodiment. As can be seen, features of the single-nanopore probe301 structure correspond to features of the twin-nanopore probe 101structure discussed herein.

If solvent 107 (with molecules 108 and 109 to be sensed) is electricallyconductive, a single-nanopore probe 301 can also be employed. Thesingle-nanopore probe 301 can be realized by using only one nanoporefrom the twin-nanopore probe 101 or specially making a single nanoporeprobe. In this case, the solvent 107 and the ionic buffer 120 are thesame.

The single-nanopore probe 301 is a scanning probe made of electricallyinsulating material. The single-nanopore probe 301 is made of one hollowchannel 103. The hollow channel 103 gradually tapers into nanopores 105at the sharp end of the single-nanopore probe 301. The single-nanoporeprobe 301 scans (e.g., back and forth or left to right) in the container106. The container 106 is filled with solvent 107 (which is the same asthe ionic buffer 120) and with molecules 108 and 109 that need to besensed as discussed herein.

The pressure-controlled reservoir 111 is filled with the solvent 107(which is the same as the ionic buffer 120) and connected to the hollowchannel 103. As noted above, the pressure-controlled reservoir 111 maybe a syringe pump, mechanical pump, motorized pump, etc. The scanningsingle-nanopore probe 301 is dipped into the container 106 to sense themolecules 108 and 109 which enter the nanopore 105 near the opening ofthe single-nanopore probe 301.

In one example, the pressure-controlled reservoir 111 may apply anegative pressure (relative to the atmosphere pressure) and/or may havea negative pressure applied to the pressure-controlled reservoir 111 todraw (vacuum) the solvent 107 (i.e. ionic buffer) into the nanopore 105.By having the pressure-controlled reservoir apply negative pressure, thesingle-nanopore probe 301 is configured to draw in both non-charged andelectrically charged particles/molecules 108 and 109, along with thesolvent 107.

Continuing the example, the solvent 107 (i.e. ionic buffer) in thecontainer 106 is pressure driven into hollow channel 103 and flows intothe pressure-controlled reservoir 111 by applying the negative pressurein pressure-controlled reservoir 111. The flow direction (caused by thenegative pressure of the reservoir 111) of the solvent 107 (i.e., ionicbuffer) is indicated by arrow 113. Molecules 108 and 109 inside thecontainer 106 are pulled into the nanopore 105 for sensing.

Electrochemical electrodes 114 and 115, such as Ag/AgCl wires, aredipped into the container 106 and reservoir 111, respectively. Voltageof voltage source 116 is applied between the two electrodes 114 and 115and the resulting ionic current is measured by ammeter 117.

While molecules 108 and 109 pass through the nanopore 105, a change inthe ionic current (measured via ammeter 117) is detected/measured. Theamount of change in the measured ionic current depends on the size andsurface charge of the molecule 108 or 109. In this way, each molecule108 or 109 is sensed as it passes through nanopore 105 as discussedherein.

In a case when the particles/molecules 108 and 109 to be measured areelectrically charged (as understood by one skilled in the art), thereservoir 111 does not need to be pressure driven as an electrical fieldcreated by voltage of the voltage source 116 drives the chargedmolecules 108 and 109 into the nanopore 105. Pressure may (only) beneeded for non-charged particles/molecules.

In one case, both negative pressure and the electric field generated byvoltage of the voltage source 116 may be utilized to capture/draw inelectrically charged molecules 108 and 109 (both charged andnon-charged) into the nanopore 105 for sensing.

FIG. 4 is a cross-sectional view of the system 100 having thetwin-nanopore probe 101 for sensing biomolecules according to anembodiment. FIG. 4 is identical to FIG. 1 except the nanopores 104 and105 are now respectively coated with organic layers 405 and 410. Theorganic layers 405 and 410 may be the same in one case, and may bedifferent in another case. The organic layers 405 and 410 may have adifferent interaction with different types of molecules 108 and 109. Forexample, the organic layer 405 and 410 may interact with a particularmolecule 108 (and/or 109) by sticking to the molecule 108, which causesa longer time duration of that particular molecule 108 inside thenanopore 105. As the ionic current (measured by the ammeter 117 when themolecule 108 is inside the nanopore 105) is monitored in real time andfrom the time trace of ionic current (graph/plot), the difference intime duration of molecules inside nanopore 105 can be resolved andemployed to differentiate molecules.

For example, if molecules 108 or 109 are proteins of viruses orantigens, then organic coating 405 or 410 can be antibodies. Ifmolecules 108 or 109 are single strand DNA molecules, organic coating405 or 410 can be complementary DNA bases or DNA oligomers.

FIG. 5 is a cross-sectional view of the system 300 having thesingle-nanopore probe 301 structure for sensing biomolecules accordingto an embodiment. FIG. 5 is identical to FIG. 3 except the nanopore 105is now coated with organic layer 410. The organic layer 410 isconfigured to interact with the molecules 108 and 109 as discussed abovefor FIG. 4.

FIG. 6 is a method 600 for sensing molecules via the twin-nanopore probe101 according to an embodiment. Reference can be made to FIGS. 1, 2, and4.

A twin-nanopore probe 101 with a first (hollow) channel 102 and a second(hollow) channel 103 is provided at block 605. A firstpressure-controlled reservoir 110 is connected to the first channel 102to generate a positive pressure 112 at block 610.

A second pressure-controlled reservoir 111 is connected to the secondchannel 103 to generate a negative pressure 113 at block 615. Acontainer 106 includes solvent 107 (fluid) with molecules 108 and 109,and a tip of the twin-nanopore probe 101 is submerged in the container106 of the solvent 107 with the molecules 108 and 109. The first channel102, the second channel 103, the first pressure-controlled reservoir110, and the second pressure-controlled reservoir 111 are filled withthe ionic buffer 120.

The first pressure-controlled reservoir 110 drives the ionic buffer 120out of the first channel 102 by the positive pressure 112 at block 620.The second pressure-controlled reservoir 111 draws in the molecules 108and 109 with the mixed ionic buffer 120 (with solvent 107 and molecules108 and 109) through the second channel 103 by the negative pressure 113at block 625.

The flow of ionic current in the twin-nanopore probe 101 is measured(via the ammeter 117) to differentiate the molecules 108 and 109 thatflow through the second channel 103 at block 630. For example, eachmolecule 108 and 109 is individually measured within the nanopore 105(by measuring the ionic current via the ammeter 117, e.g., detecting thechange in ionic current from a baseline value (waveform) when nomolecule 108/109 is in the nanopore 105 to the modified ionic current(waveform) when the particular molecule 108/109 is inside the nanopore105). Voltage of the voltage source 116 is applied to generate the ioniccurrent via electrodes 114 and 115.

Further, the method includes defining a region (e.g., the area 118)according to the positive pressure 112 generated by the firstpressure-controlled reservoir 110 and the negative pressure 113generated by the second pressure-controlled reservoir 111. Accordingly,the region (area 118) comprises the molecules 108 and 109 to be drawninto the second channel 103 via the nanopore 105.

The method in which the first channel 102 comprises an elongated section(e.g., the tubular section between the reservoir 110 and the nanopore104) connected to a first nanopore 104, and the first nanopore 104 is anexit for the positive pressure 112 generated by the firstpressure-controlled reservoir 110. The method in which the secondchannel 103 comprises an elongated section (e.g., the tubular sectionbetween the reservoir 111 and the nanopore 105) connected to a secondnanopore 105, and the second nanopore 105 is an entrance (inlet) for thenegative pressure 113 generated by the second pressure-controlledreservoir 111.

The method in which inner surfaces of the second nanopore 105 are coatedwith an organic layer 410, and the organic layer 410 interactsdifferently with the different types of molecules 108 and 109.

The method in which a first electrode 114 is in the firstpressure-controlled reservoir 110 and a second electrode 115 is in thesecond pressure-controlled reservoir 111, and a voltage source 116 isconnected to the first electrode 114 and the second electrode 115. Thevoltage source 116 generates the ionic current to measure (via theammeter 117) each of the molecules 108 and 109 that flow through thesecond channel 103 (e.g., while in the nanopore 105).

FIG. 7 is a method 700 for sensing molecules via the singe-nanoporeprobe 301 structure according to an embodiment. Reference can be made toFIGS. 2 and 3. In this case, the solvent 107 is electrically conductingand is the same as the ionic buffer 120.

The single-nanopore probe 301 structure includes a channel 103 at block705. A pressure-controlled reservoir 111 is connected to the channel103. A container 106 comprises solvent 107 (i.e., ionic buffer) withmolecules 108 and 109, and the tip of the single-nanopore probe 301 issubmerged in the container 106 of the solvent 107 (ionic buffer) withthe molecules 108 and 109. The channel 103 and the pressure-controlledreservoir 111 are filled with the same solvent 107 (ionic buffer) (e.g.,but without the molecules 108 and 109).

The molecules 108 and 109 are drawn (pulled) into the channel 103 by thenegative pressure 113 inside the single-nanopore probe 301 (and thecontainer 106) at block 710. A flow of ionic current through thesingle-nanopore probe 301 is measured (via the ammeter 117) todifferentiate the molecules 108 and 109 that flow into the channel 103at block 715.

The method in which one electrode 115 is in the pressure-controlledreservoir and another electrode 114 is in the container 106, and avoltage source 116 is connected to one electrode 115 and the otherelectrode 114. The method in which the voltage source 116generates/causes the ionic current to differentiate the molecules 108and 109 (while in the nanopore 105) that flow into the channel 103.

FIG. 8 illustrates an example of a computer 800 (e.g., as part of thecomputer setup for testing and analysis) having capabilities, which maybe included in exemplary embodiments. Various methods, procedures,modules, flow diagrams, tools, applications, circuits, elements, andtechniques discussed herein may also incorporate and/or utilize thecapabilities of the computer 800. Moreover, capabilities of the computer800 may be utilized to implement features of exemplary embodimentsdiscussed herein. One or more of the capabilities of the computer 800may be utilized to implement, to connect to, and/or to support anyelement discussed herein (as understood by one skilled in the art) inFIGS. 1-7. For example, the computer 800 which may be any type ofcomputing device and/or test equipment (including ammeters, voltagesources, connectors, etc.). Input/output device 870 (having propersoftware and hardware) of computer 800 may include and/or be coupled tothe nanodevices and structures discussed herein via cables, plugs,wires, electrodes, etc. Also, the communication interface of theinput/output devices 870 comprises hardware and software forcommunicating with, operatively connecting to, reading, and/orcontrolling voltage sources, ammeters, and ionic current traces (e.g.,magnitude and time duration of ionic current), etc., as discussedherein. The user interfaces of the input/output device 870 may include,e.g., a track ball, mouse, pointing device, keyboard, touch screen,etc., for interacting with the computer 800, such as inputtinginformation, making selections, independently controlling differentvoltages sources, and/or displaying, viewing and recording ionic currenttraces for each base, molecule, biomolecules, etc.

Generally, in terms of hardware architecture, the computer 800 mayinclude one or more processors 810, computer readable storage memory820, and one or more input and/or output (I/O) devices 870 that arecommunicatively coupled via a local interface (not shown). The localinterface can be, for example but not limited to, one or more buses orother wired or wireless connections, as is known in the art. The localinterface may have additional elements, such as controllers, buffers(caches), drivers, repeaters, and receivers, to enable communications.Further, the local interface may include address, control, and/or dataconnections to enable appropriate communications among theaforementioned components.

The processor 810 is a hardware device for executing software that canbe stored in the memory 820. The processor 810 can be virtually anycustom made or commercially available processor, a central processingunit (CPU), a data signal processor (DSP), or an auxiliary processoramong several processors associated with the computer 800, and theprocessor 810 may be a semiconductor based microprocessor (in the formof a microchip) or a macroprocessor.

The computer readable memory 820 can include any one or combination ofvolatile memory elements (e.g., random access memory (RAM), such asdynamic random access memory (DRAM), static random access memory (SRAM),etc.) and nonvolatile memory elements (e.g., ROM, erasable programmableread only memory (EPROM), electronically erasable programmable read onlymemory (EEPROM), programmable read only memory (PROM), tape, compactdisc read only memory (CD-ROM), disk, diskette, cartridge, cassette orthe like, etc.). Moreover, the memory 820 may incorporate electronic,magnetic, optical, and/or other types of storage media. Note that thememory 820 can have a distributed architecture, where various componentsare situated remote from one another, but can be accessed by theprocessor 810.

The software in the computer readable memory 820 may include one or moreseparate programs, each of which comprises an ordered listing ofexecutable instructions for implementing logical functions. The softwarein the memory 820 includes a suitable operating system (O/S) 850,compiler 840, source code 830, and one or more applications 860 of theexemplary embodiments. As illustrated, the application 860 comprisesnumerous functional components for implementing the features, processes,methods, functions, and operations of the exemplary embodiments.

The operating system 850 may control the execution of other computerprograms, and provides scheduling, input-output control, file and datamanagement, memory management, and communication control and relatedservices.

The application 860 may be a source program, executable program (objectcode), script, or any other entity comprising a set of instructions tobe performed. When a source program, then the program is usuallytranslated via a compiler (such as the compiler 840), assembler,interpreter, or the like, which may or may not be included within thememory 820, so as to operate properly in connection with the O/S 850.Furthermore, the application 860 can be written as (a) an objectoriented programming language, which has classes of data and methods, or(b) a procedure programming language, which has routines, subroutines,and/or functions.

The I/O devices 870 may include input devices (or peripherals) such as,for example but not limited to, a mouse, keyboard, scanner, microphone,camera, etc. Furthermore, the I/O devices 870 may also include outputdevices (or peripherals), for example but not limited to, a printer,display, etc. Finally, the I/O devices 870 may further include devicesthat communicate both inputs and outputs, for instance but not limitedto, a NIC or modulator/demodulator (for accessing remote devices, otherfiles, devices, systems, or a network), a radio frequency (RF) or othertransceiver, a telephonic interface, a bridge, a router, etc. The I/Odevices 870 also include components for communicating over variousnetworks, such as the Internet or an intranet. The I/O devices 870 maybe connected to and/or communicate with the processor 810 utilizingBluetooth connections and cables (via, e.g., Universal Serial Bus (USB)ports, serial ports, parallel ports, FireWire, HDMI (High-DefinitionMultimedia Interface), etc.).

In exemplary embodiments, where the application 860 is implemented inhardware, the application 860 can be implemented with any one or acombination of the following technologies, which are each well known inthe art: a discrete logic circuit(s) having logic gates for implementinglogic functions upon data signals, an application specific integratedcircuit (ASIC) having appropriate combinational logic gates, aprogrammable gate array(s) (PGA), a field programmable gate array(FPGA), etc.

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. It will be further understood that the terms “comprises”and/or “comprising,” when used in this specification, specify thepresence of stated features, integers, steps, operations, elements,and/or components, but do not preclude the presence or addition of onemore other features, integers, steps, operations, element components,and/or groups thereof.

The corresponding structures, materials, acts, and equivalents of allmeans or step plus function elements in the claims below are intended toinclude any structure, material, or act for performing the function incombination with other claimed elements as specifically claimed. Thedescription of the present invention has been presented for purposes ofillustration and description, but is not intended to be exhaustive orlimited to the invention in the form disclosed. Many modifications andvariations will be apparent to those of ordinary skill in the artwithout departing from the scope and spirit of the invention. Theembodiment was chosen and described in order to best explain theprinciples of the invention and the practical application, and to enableothers of ordinary skill in the art to understand the invention forvarious embodiments with various modifications as are suited to theparticular use contemplated

The flow diagrams depicted herein are just one example. There may bemany variations to this diagram or the steps (or operations) describedtherein without departing from the spirit of the invention. Forinstance, the steps may be performed in a differing order or steps maybe added, deleted or modified. All of these variations are considered apart of the claimed invention.

While the preferred embodiment to the invention had been described, itwill be understood that those skilled in the art, both now and in thefuture, may make various improvements and enhancements which fall withinthe scope of the claims which follow. These claims should be construedto maintain the proper protection for the invention first described.

What is claimed is:
 1. A method for sensing molecules, the methodcomprising: providing a twin-nanopore probe comprising a first channeland a second channel; generating a positive pressure by a firstpressure-controlled reservoir connected to the first channel; generatinga negative pressure by a second pressure-controlled reservoir connectedto the second channel; wherein a container comprises solvent with themolecules, a tip of the twin-nanopore probe being submerged in thecontainer of the ionic fluid with the molecules; and wherein the firstchannel, the second channel, the first pressure-controlled reservoir,and the second pressure-controlled reservoir are filled with the ionicfluid; driving the ionic fluid out of the first channel by the firstpressure-controlled reservoir; drawing in the ionic fluid, mixed withthe molecules and the solvent, through the second channel by the secondpressure-controlled reservoir; and measuring a flow of ionic current inthe twin-nanopore probe to differentiate the molecules that flow throughthe second channel.
 2. The method of claim 1, further comprisingdefining a region according to the positive pressure generated by thefirst pressure-controlled reservoir and the negative pressure generatedby the second pressure-controlled reservoir;
 3. The method of claim 2,wherein the region comprises the molecules to be drawn into the secondchannel.
 4. The method of claim 1, wherein the first channel comprisesan elongated section connected to a first nanopore.
 5. The method ofclaim 4, wherein the first nanopore is an exit for the positive pressuregenerated by the first pressure-controlled reservoir.
 6. The method ofclaim 5, wherein the second channel comprises an elongated sectionconnected to a second nanopore.
 7. The method of claim 6, wherein thesecond nanopore is an entrance for the negative pressure generated bythe second pressure-controlled reservoir.
 8. The method of claim 7,wherein inner surfaces of the second nanopore are coated with an organiclayer; and wherein the organic layer interacts differently with themolecules.
 9. The method of claim 1, wherein a first electrode is in thefirst pressure-controlled reservoir and a second electrode is in thesecond pressure-controlled reservoir.
 10. The method of claim 9, whereina voltage source is connected to the first electrode and the secondelectrode.
 11. The method of claim 10, wherein the voltage sourcegenerates the ionic current to measure each of the molecules that flowthrough the second channel.
 12. A method for sensing molecules, themethod comprising: providing a single-nanopore probe comprising achannel; wherein a reservoir is connected to the channel; wherein acontainer comprises ionic fluid with the molecules, a tip of thesingle-nanopore probe being submerged in the container of the ionicfluid with the molecules; and wherein the channel and the reservoir arefilled with the ionic fluid; drawing the molecules into the channel by anegative pressure inside the single-nanopore probe; and measuring a flowof ionic current through the single-nanopore probe to differentiate themolecules that flow into the channel.
 13. The method of claim 12,wherein a first electrode is in the reservoir and a second electrode isin the container.
 14. The method of claim 13, wherein a voltage sourceis connected to the first electrode and the second electrode.
 15. Themethod of claim 14, wherein the voltage source generates the ioniccurrent to differentiate the molecules that flow into the channel.